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相关概念视频

Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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相关实验视频

Updated: Jun 7, 2025

Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods
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基于分子动力学模拟和马尔科夫算法SHP2-E76K结合点的预测.

Si-Pei Zhang1, Li-Juan Chen1, Zhen-Liang Shi2

  • 1Department of Pharmacy, Tianjin Chest Hospital, Tianjin, China.

Journal of biomolecular structure & dynamics
|November 19, 2024
PubMed
概括

这项研究揭示了SHP099与SHP2-E76K突变的动态结合,这对于向固体瘤至关重要. 了解这种相互作用有助于开发更有效的SHP2-E76K抑制剂.

关键词:
在MM/PBSA中,可以选择MM/PBSA.马尔科夫模型的模型在SHP2-E76K中使用.过渡路径理论 过渡路径理论雨抽样是统一的抽样方式.

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科学领域:

  • 生物化学 生物化学
  • 分子生物学分子生物学
  • 药理学 药理学是指药理学的学科.

背景情况:

  • PTPN11基因编码SHP2,一种蛋白质酸酶,当突变为SHP2-E76K时,它与各种固体瘤有关.
  • SHP2-E76K是一个有前途的药物标,但目前尚无有效的抑制剂.
  • 虽然SHP099与SHP2-E76K的静态晶体结构存在,但其动态结合行为仍然没有特征.

研究的目的:

  • 阐明抑制剂SHP099与SHP2-E76K酶之间的动态相互作用.
  • 在原子层面上确定SHP099在SHP2-E76K内的精确活性结合点.
  • 为设计更强大的SHP2-E76K抑制剂提供见解.

主要方法:

  • 用分子动力学 (MD) 模拟来捕捉SHP099-SHP2-E76K复合物的动态行为.
  • 马尔科夫状态建模 (MSM) 用于分析抑制剂结合的动态途径.
  • 对酶-抑制剂相互作用的原子细节进行了表征.

主要成果:

  • 该研究描述了SHP099与SHP2-E76K活性部位结合的动力学.
  • 确定了控制酶抑制剂复合物的关键原子相互作用.
  • 揭示了动态结合过程和活性位点相互作用.

结论:

  • 这项研究提供了对SHP099与SHP2-E76K结合的详细动态理解.
  • 这些发现为SHP2-E76K.的酶基质相互作用提供了关键的见解.
  • 这项研究为合理设计新型和更有效的SHP2-E76K抑制剂奠定了基础.